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"https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10534", "recommended_name": { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "stomach cancer", "description": "A gastrointestinal system cancer that is located_in the stomach." }, "synonyms": [ { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric cancer", "description": "" }, { "id": "DOID:10534", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10534", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "A primary or metastatic malignant neoplasm involving the stomach." }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca lesser curvature - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "GC", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "cancer of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer risk after h. pylori infection", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "gastric cancer, somatic", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumor", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant gastric tumour", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant stomach neoplasm", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumor of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of body of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of greater curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of lesser curve of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant tumour of the stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "stomach cancer", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "Ca body - stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "ca greater curvature of stomach", "description": "" }, { "id": "MONDO:0001056", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001056", "name": "malignant neoplasm of body of stomach", "description": "" }, { "id": "MIM:613659", "resource": "MIM", "url": "https://www.omim.org/entry/613659", "name": "Gastric cancer", "description": "Gastric cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" }, { "id": "10534", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10534" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumor of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "oesophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", 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"resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", 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Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": 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"https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, 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"https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease 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"https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 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}, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, 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"https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" 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"MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": 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"familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", 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"MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" 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"description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { 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cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": 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"url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. 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"description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung 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"Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { "evidence": [ { "id": "Q8N7R1", "database": "BioMuta", "url": "https://hivelab.biochemistry.gwu.edu/biomuta/proteinview/Q8N7R1" } ], "glycoeffect": [], "subjects_tested": "719", "subjects_positive": "1", "frequency": "0.1", "sequence_org": "A", "sequence_mut": "V", "comment": "Somatic mutation passed 1 filters: num. of cancers (5).", "chr_id": "7", "chr_pos": "53036096", "ref_nt": "C", "alt_nt": "T", "minor_allelic_frequency": "", "site_lbl": "A142", "disease": [ { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. 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"https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of Brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant tumor of adult brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "primary malignant neoplasm of brain", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "tumor of the Brain", "description": "" } ], "unlinked_id_list": [ "DOID:4203", "DOID:3541", "DOID:4706", "DOID:1659", "DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. 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"MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "" }, { "id": "MIM:114480", "resource": "MIM", "url": "https://www.omim.org/entry/114480", "name": "Breast cancer", "description": "Breast cancer" } ], "unlinked_id_list": [ "DOID:3017", "DOID:0050938" ], "evidence": [ { "id": "1612", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1612" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant 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"malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:11934", "recommended_name": { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck cancer", "description": "An organ system cancer that arises in the head or neck region. This region includes the nasal cavity, sinuses, lips, mouth, salivary glands, throat, or larynx." }, "synonyms": [ { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head and neck tumours", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "head/neck neoplasm", "description": "" }, { "id": "DOID:11934", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11934", "name": "tumor of head and neck", "description": "" } ], "unlinked_id_list": [ "DOID:1542" ], "evidence": [ { "id": "11934", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:11934" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, susceptibility to, autosomal 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Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1319", "recommended_name": { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain cancer", "description": "A central nervous system cancer that is characterized by the growth of abnormal cells in the tissues of the brain." }, "synonyms": [ { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "BT - Brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "adult malignant brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "brain neoplasm, adult", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant brain tumour", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain neoplasm", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant primary brain tumor", "description": "" }, { "id": "DOID:1319", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1319", "name": "malignant 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"name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": 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"malignant tumour of abdominal oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of proximal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant tumour of the middle third of the oesophagus", "description": "" }, { "id": "MIM:133239", "resource": "MIM", "url": "https://www.omim.org/entry/133239", "name": "Esophageal cancer", "description": "Esophageal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "5041", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:5041" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] }, { 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"MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", 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"resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). 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"MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate 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Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. 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"https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, 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"malignant tumour of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumour of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "CRC", "description": "" }, { "id": "MIM:114500", "resource": "MIM", "url": "https://www.omim.org/entry/114500", "name": "Colorectal cancer", "description": "Colorectal cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "9256", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:9256" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": 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"MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": 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"https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. 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"prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, 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cancer, somatic", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumor", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovarian malignant tumour", "description": "" }, { "id": "MONDO:0008170", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008170", "name": "ovary cancer", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "OVCAS1", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to", "description": "" }, { "id": "MONDO:0011931", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011931", "name": "ovarian cancer, susceptibility to, 1", "description": "" }, { "id": "MIM:167000", "resource": "MIM", "url": "https://www.omim.org/entry/167000", "name": "Ovarian cancer", "description": "Ovarian cancer" } ], "unlinked_id_list": [ "DOID:2151" ], "evidence": [ { "id": "2394", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2394" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": 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"resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectum cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectal tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant colorectum neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large bowel tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine neoplasm", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumor", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant large intestine tumour", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant neoplasm of the large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "malignant tumor of large bowel", "description": "" 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"MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": 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"resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", 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"https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). 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"https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": 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"https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary 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"MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" 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"" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": 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cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": 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"Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that 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"description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", 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"MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": 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"https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": 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"https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, 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"MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "264", "end_pos": "264" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "5", "end_pos": "5" } ] }, { "type": "snv", "site_list": [ { "start_pos": "122", "end_pos": "122" }, { "start_pos": "131", "end_pos": "131" }, { "start_pos": "155", "end_pos": "155" }, { "start_pos": "165", "end_pos": "165" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "180", "end_pos": "180" }, { "start_pos": "186", "end_pos": "186" }, { "start_pos": "264", "end_pos": "264" }, { "start_pos": "266", "end_pos": "266" }, { "start_pos": "280", "end_pos": "280" }, { "start_pos": "287", "end_pos": "287" }, { "start_pos": 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"id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1793", "recommended_name": { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic cancer", "description": "An endocrine gland cancer located_in the pancreas." }, "synonyms": [ { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "Ca tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of body of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of head of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "malignant neoplasm of tail of pancreas", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreas neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic neoplasm", "description": "" }, { "id": "DOID:1793", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1793", "name": "pancreatic tumor", "description": "" } ], "unlinked_id_list": [ "DOID:1795" ], "evidence": [ { "id": "1793", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1793" } ] }, { "disease_id": "DOID:4362", "recommended_name": { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical cancer", "description": "A female reproductive organ cancer that is located_in the cervix." }, "synonyms": [ { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervical neoplasm", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "cervix uteri cancer", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "neoplasm of uterine cervix", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "tumor of the Cervix Uteri", "description": "" }, { "id": "DOID:4362", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4362", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer", "description": "A primary or metastatic malignant neoplasm involving the cervix." }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cancer of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "cervical cancer, somatic", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervical tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant cervix uteri tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant neoplasm of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumor of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the cervix uteri", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of the uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant tumour of uterine cervix", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix neoplasm", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumor", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "malignant uterine cervix tumour", "description": "" }, { "id": "MONDO:0002974", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0002974", "name": "uterine cervix cancer", "description": "" }, { "id": "MIM:603956", "resource": "MIM", "url": "https://www.omim.org/entry/603956", "name": "Cervical cancer", "description": "Cervical cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "4362", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4362" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": 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"https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": 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"MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:363", "recommended_name": { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine cancer", "description": "A female reproductive organ cancer that is located_in the uterus." }, "synonyms": [ { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": 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], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Extracellular arginine availability modulates eIF2\u03b1 O-GlcNAcylation and heme oxygenase 1 translation for cellular homeostasis.", "journal": "Journal of biomedical science", "date": "2023-05-22", "authors": "Hung Yu-Wen, Ouyang Ching, Ping Xiaoli, Qi Yue, Wang Yi-Chang, Kung Hsing-Jien, Ann David K", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" }, { "database": "O-GlcNAc Atlas", "id": "P05387", "url": "https://oglcnac.org/atlas/detail/P05387" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "O-GlcNAc-induced nuclear translocation of hnRNP-K is associated with progression and metastasis of cholangiocarcinoma.", "journal": "Molecular oncology", "date": "2019", "authors": "Phoomak C, Park D, Silsirivanit A, Sawanyawisuth K, Vaeteewoottacharn K, Detarya M, Wongkham C, Lebrilla CB, Wongkham S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "30444036", "url": "https://glygen.org/publication/PubMed/30444036" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" }, { "database": "O-GlcNAc Atlas", "id": "P05387", "url": "https://oglcnac.org/atlas/detail/P05387" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" }, { "database": "O-GlcNAc Atlas", "id": "P05387", "url": "https://oglcnac.org/atlas/detail/P05387" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" }, { "database": "O-GlcNAc Atlas", "id": "P05387", "url": "https://oglcnac.org/atlas/detail/P05387" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" }, { "database": "O-GlcNAc Atlas", "id": "P05387", "url": "https://oglcnac.org/atlas/detail/P05387" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with 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"https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "21740066", "url": "https://glygen.org/publication/PubMed/21740066" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "GlcNAcylation of histone H2B facilitates its monoubiquitination.", "journal": "Nature", "date": "2011", "authors": "Fujiki R, Hashiba W, Sekine H, Yokoyama A, Chikanishi T, Ito S, Imai Y, Kim J, He HH, Igarashi K, Kanno J, Ohtake F, Kitagawa H, Roeder RG, Brown M, Kato S", "evidence": [ { 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"journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": 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"journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" }, { "database": "O-GlcNAc Atlas", "id": "P05387", "url": "https://oglcnac.org/atlas/detail/P05387" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" }, { "database": "O-GlcNAc Atlas", "id": "P05387", "url": "https://oglcnac.org/atlas/detail/P05387" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" }, { "database": "O-GlcNAc Atlas", "id": "P05387", "url": "https://oglcnac.org/atlas/detail/P05387" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with 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Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" }, { "database": "O-GlcNAc Atlas", "id": "P05387", "url": "https://oglcnac.org/atlas/detail/P05387" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": 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Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" }, { "database": "O-GlcNAc Atlas", "id": "P05387", "url": "https://oglcnac.org/atlas/detail/P05387" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Extracellular arginine availability modulates eIF2\u03b1 O-GlcNAcylation and heme oxygenase 1 translation for cellular homeostasis.", "journal": "Journal of biomedical science", "date": "2023-05-22", "authors": "Hung Yu-Wen, Ouyang Ching, Ping Xiaoli, Qi Yue, Wang Yi-Chang, Kung Hsing-Jien, Ann David K", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "37217939", "url": "https://glygen.org/publication/PubMed/37217939" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" }, { "database": "O-GlcNAc Atlas", "id": "P05387", "url": "https://oglcnac.org/atlas/detail/P05387" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "O-GlcNAc-induced nuclear translocation of hnRNP-K is associated with progression and metastasis of cholangiocarcinoma.", "journal": "Molecular oncology", "date": "2019", "authors": "Phoomak C, Park D, Silsirivanit A, Sawanyawisuth K, Vaeteewoottacharn K, Detarya M, Wongkham C, Lebrilla CB, Wongkham S", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "30444036", "url": "https://glygen.org/publication/PubMed/30444036" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": 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Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" }, { "database": "O-GlcNAc Atlas", "id": "P05387", "url": "https://oglcnac.org/atlas/detail/P05387" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" }, { "database": "O-GlcNAc Atlas", "id": "P05387", "url": "https://oglcnac.org/atlas/detail/P05387" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" }, { "database": "O-GlcNAc Atlas", "id": "P05387", "url": "https://oglcnac.org/atlas/detail/P05387" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" }, { "database": "O-GlcNAc Atlas", "id": "P05387", "url": "https://oglcnac.org/atlas/detail/P05387" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Combining high-energy C-trap dissociation and electron transfer dissociation for protein O-GlcNAc modification site assignment.", "journal": "Journal of proteome research", "date": "2011", "authors": "Zhao P, Viner R, Teo CF, Boons GJ, Horn D, Wells L", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": 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"journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=P05387" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "P05387", "url": 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"MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", 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"https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1612", "recommended_name": { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast cancer", "description": "An organ system cancer that originates in the mammary gland." }, "synonyms": [ { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "breast tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant neoplasm of breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "malignant tumor of the breast", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary cancer", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "mammary tumor", "description": "" }, { "id": "DOID:1612", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1612", "name": "primary breast cancer", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "hereditary breast carcinoma", "description": "Breast carcinoma that has developed in relatives of patients with history of breast carcinoma." }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer susceptibility, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, early-onset, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, invasive ductal, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, lobular, somatic", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, male, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0016419", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0016419", "name": "breast cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": 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"id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "LNCR1", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility", "description": "" }, { "id": "MONDO:0012159", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012159", "name": "lung cancer susceptibility 1", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "LNCR3", "description": "" }, { "id": "MONDO:0012942", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012942", "name": "lung cancer susceptibility 3", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "LNCR4", "description": "" }, { "id": "MONDO:0012955", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012955", "name": "lung cancer susceptibility 4", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "LNCR5", "description": "" }, { "id": "MONDO:0013631", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0013631", "name": "lung cancer susceptibility 5", "description": "" }, { "id": "MIM:211980", "resource": "MIM", "url": "https://www.omim.org/entry/211980", "name": "Lung cancer", "description": "Lung cancer" } ], "unlinked_id_list": [ "DOID:4765" ], "evidence": [ { "id": "1324", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1324" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": 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"description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { 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"MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). 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"resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 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}, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. 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It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": 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"MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary 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Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { 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[ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "title": "Aspartate Residues Far from the Active Site Drive O-GlcNAc Transferase Substrate Selection.", "journal": "Journal of the American Chemical Society", "date": "2019", "authors": "Joiner CM, Levine ZG, Aonbangkhen C, Woo CM, Walker S", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31373491", "url": "https://glygen.org/publication/PubMed/31373491" } ] } ], "crossref": [ { "id": "29237092", "url": 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proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. 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"Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "GlyConnect", "id": "2891", "url": "https://glyconnect.expasy.org/browser/proteins/2891" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" 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"title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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"date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": 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"type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" 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Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] 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Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc 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Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { 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"https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { 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in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. 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"https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "GlyConnect", "id": "2891", "url": "https://glyconnect.expasy.org/browser/proteins/2891" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "title": "Cell-type-specific labeling and profiling of glycans in living mice.", "journal": "Nature chemical biology", "date": "2022-06", "authors": "Fan Xinqi, Song Qitao, Sun De-En, Hao Yi, Wang Jingyang, Wang Chunting, Chen Xing", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35513511", "url": "https://glygen.org/publication/PubMed/35513511" } ] }, { "title": "O-GlcNAcylation of Raptor transduces glucose signals to mTORC1.", "journal": "Molecular cell", "date": "2023-08-17", "authors": "Xu Chenchen, Pan Xiaoqing, Wang Dong, Guan Yuanyuan, Yang Wenyu, Chen Xing, Liu Ying", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260" } ] } ], "crossref": [ { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": 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"https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": 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"journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. 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O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" 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}, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { 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{ "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "GlyConnect", "id": "2891", "url": "https://glyconnect.expasy.org/browser/proteins/2891" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "title": "Cell-type-specific labeling and profiling of glycans in living mice.", "journal": "Nature chemical biology", "date": "2022-06", "authors": "Fan Xinqi, Song Qitao, Sun De-En, Hao Yi, Wang Jingyang, Wang Chunting, Chen Xing", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35513511", "url": "https://glygen.org/publication/PubMed/35513511" } ] }, { "title": "O-GlcNAcylation of Raptor transduces glucose signals to mTORC1.", "journal": "Molecular cell", "date": "2023-08-17", "authors": "Xu Chenchen, Pan Xiaoqing, Wang Dong, Guan Yuanyuan, Yang Wenyu, Chen Xing, Liu Ying", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260" } ] } ], "crossref": [ { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": 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Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] 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Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc 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Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { 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"https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { 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in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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Per-O-Acetylated Unnatural Monosaccharides during Metabolic Glycan Labeling.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2018", "authors": "Qin W, Qin K, Fan X, Peng L, Hong W, Zhu Y, Lv P, Du Y, Huang R, Han M, Cheng B, Liu Y, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092" } ] }, { "title": "An Isotope-Coded Photocleavable Probe for Quantitative Profiling of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": 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D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "GlyConnect", "id": "2891", "url": "https://glyconnect.expasy.org/browser/proteins/2891" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Spatiotemporal 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"https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { 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Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, 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"https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { 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in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": 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Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, 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"https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { 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in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { 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"https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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}, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc 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Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification 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General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": 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protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc 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Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "title": "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.", "journal": "Science signaling", "date": "2009", "authors": "Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK", "evidence": [ { "database": "UniProtKB", "id": "Q5VT52", "url": "https://www.uniprot.org/uniprotkb/Q5VT52" }, { "database": "iPTMnet", "id": "Q5VT52", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52" } ], "reference": [ { "type": 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"2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": 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"date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": 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General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { 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of Protein O-GlcNAcylation.", "journal": "ACS chemical biology", "date": "2019", "authors": "Li J, Li Z, Duan X, Qin K, Dang L, Sun S, Cai L, Hsieh-Wilson LC, Wu L, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550" } ] }, { "title": "Rapid and large-scale glycopeptide enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": 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"https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc 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Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers 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Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, 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Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "GlyConnect", "id": "2891", "url": "https://glyconnect.expasy.org/browser/proteins/2891" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q5VT52", "url": "https://www.uniprot.org/uniprotkb/Q5VT52" }, { "database": "iPTMnet", "id": "Q5VT52-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.", "journal": "Science signaling", "date": "2009", "authors": "Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK", "evidence": [ { "database": "UniProtKB", "id": "Q5VT52", "url": "https://www.uniprot.org/uniprotkb/Q5VT52" }, { "database": "iPTMnet", "id": "Q5VT52", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "Q5VT52", "url": "https://www.uniprot.org/uniprotkb/Q5VT52" }, { "database": "iPTMnet", "id": "Q5VT52", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Pan C, Olsen JV, Daub H, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q5VT52-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "UniProtKB", "id": "Q5VT52", "url": "https://www.uniprot.org/uniprotkb/Q5VT52" }, { "database": "iPTMnet", "id": "Q5VT52-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] } ], "crossref": [ { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": 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one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, 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"https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { 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in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "GlyConnect", "id": "2891", "url": "https://glyconnect.expasy.org/browser/proteins/2891" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Spatiotemporal 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General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { 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in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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"2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": 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Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { 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"https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "GlyConnect", "id": "2891", "url": "https://glyconnect.expasy.org/browser/proteins/2891" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" 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"journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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{ "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "GlyConnect", "id": "2891", "url": "https://glyconnect.expasy.org/browser/proteins/2891" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" 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"journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": 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and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": 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General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { 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"Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, 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"https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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"https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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"2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": 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General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { 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in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "GlyConnect", "id": "2891", "url": "https://glyconnect.expasy.org/browser/proteins/2891" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" 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"type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" 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"reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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"Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "GlyConnect", "id": "2891", "url": "https://glyconnect.expasy.org/browser/proteins/2891" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] } ], "crossref": [ { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" 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materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { 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reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, 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General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": 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Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { 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"https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "GlyConnect", "id": "2891", "url": "https://glyconnect.expasy.org/browser/proteins/2891" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "title": "Spatial and temporal proteomics reveals the distinct distributions and dynamics of O-GlcNAcylated proteins.", "journal": "Cell reports", "date": "2022-06-14", "authors": "Xu Senhan, Tong Ming, Suttapitugsakul Suttipong, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054" } ] }, { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q5VT52", "url": "https://www.uniprot.org/uniprotkb/Q5VT52" }, { "database": "iPTMnet", "id": "Q5VT52-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.", "journal": "Science signaling", "date": "2009", "authors": "Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK", "evidence": [ { "database": "UniProtKB", "id": "Q5VT52", "url": "https://www.uniprot.org/uniprotkb/Q5VT52" }, { "database": "iPTMnet", "id": "Q5VT52", "url": 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"date": "2011", "authors": "Rigbolt KT, Prokhorova TA, Akimov V, Henningsen J, Johansen PT, Kratchmarova I, Kassem M, Mann M, Olsen JV, Blagoev B", "evidence": [ { "database": "UniProtKB", "id": "Q5VT52", "url": "https://www.uniprot.org/uniprotkb/Q5VT52" }, { "database": "iPTMnet", "id": "Q5VT52", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "21406692", "url": "https://glygen.org/publication/PubMed/21406692" } ] }, { "title": "Large-scale characterization of HeLa cell nuclear phosphoproteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2004", "authors": "Beausoleil SA, Jedrychowski M, Schwartz D, Elias JE, Villen J, Li J, Cohn MA, Cantley LC, Gygi SP", "evidence": [ { "database": "iPTMnet", "id": "Q5VT52-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52-1" } ], "reference": [ { "type": "PubMed", "id": "15302935", "url": "https://glygen.org/publication/PubMed/15302935" } ] }, { "title": "Motif-specific sampling of phosphoproteomes.", "journal": "Journal of proteome research", "date": "2008", "authors": "Ruse CI, McClatchy DB, Lu B, Cociorva D, Motoyama A, Park SK, Yates JR 3rd", "evidence": [ { "database": "iPTMnet", "id": "Q5VT52-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52-1" } ], "reference": [ { "type": "PubMed", "id": "18452278", "url": "https://glygen.org/publication/PubMed/18452278" } ] }, { "title": "Phosphoproteome analysis of the human Chang liver cells using SCX and a complementary mass spectrometric strategy.", "journal": "Proteomics", "date": "2008", "authors": "Sui S, Wang J, Yang B, Song L, Zhang J, Chen M, Liu J, Lu Z, Cai Y, Chen S, Bi W, Zhu Y, He F, Qian X", "evidence": [ { "database": "iPTMnet", "id": "Q5VT52-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52-1" } ], "reference": [ { "type": "PubMed", "id": "18491316", "url": 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"https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Phosphoproteomic analysis of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Brill LM, Xiong W, Lee KB, Ficarro SB, Crain A, Xu Y, Terskikh A, Snyder EY, Ding S", "evidence": [ { "database": "iPTMnet", "id": "Q5VT52-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52-1" } ], "reference": [ { "type": "PubMed", "id": "19664994", "url": "https://glygen.org/publication/PubMed/19664994" } ] }, { "title": "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "evidence": [ { "database": "iPTMnet", "id": "Q5VT52-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52-1" } ], "reference": [ { "type": "PubMed", "id": "19664995", "url": 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"reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { 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Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": 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in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "title": "Spatial and temporal proteomics reveals the distinct distributions and dynamics of O-GlcNAcylated proteins.", "journal": "Cell reports", "date": "2022-06-14", "authors": "Xu Senhan, Tong Ming, Suttapitugsakul Suttipong, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054" } ] }, { "title": "A quantitative atlas of mitotic phosphorylation.", 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Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "GlyConnect", "id": "2891", "url": "https://glyconnect.expasy.org/browser/proteins/2891" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "title": "Methods for Enrichment and Assignment of N-Acetylglucosamine Modification Sites.", "journal": "Molecular & cellular proteomics : MCP", "date": "2021", "authors": "Maynard JC, Chalkley RJ", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32938750", "url": "https://glygen.org/publication/PubMed/32938750" } ] }, { "title": "Spatial and temporal proteomics reveals the distinct distributions and dynamics of 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Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional 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General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { 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in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { 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O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": 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"evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": 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Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", 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General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { 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Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, 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"https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { 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in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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enrichment strategy based on chemical ligation.", "journal": "National science review", "date": "2024-11", "authors": "Xiong Yingying, Lu Zhuoer, Shao Yuyin, Meng Peiyi, Wang Guoli, Zhou Xinwen, Yao Jun, Bao Huimin, Lu Haojie", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244" } ] }, { "title": "Truncation of the TPR domain of OGT alters substrate and glycosite selection.", "journal": "Analytical and bioanalytical chemistry", "date": "2021", "authors": "Ramirez DH, Yang B, D'Souza AK, Shen D, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712" } ] }, { "title": "Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells.", "journal": "ACS chemical biology", "date": "2020", "authors": "Ramirez DH, Aonbangkhen C, Wu HY, Naftaly JA, Tang S, O'Meara TR, Woo CM", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511" } ] }, { "title": "Discovery of O-GlcNAc-modified proteins in published large-scale proteome data.", "journal": "Molecular & cellular proteomics : MCP", "date": "2012", "authors": "Hahne H, Gholami AM, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428" } ] }, { "title": "Design and Preparation of Novel Nitro-Oxide-Grafted Nanospheres with Enhanced Hydrogen Bonding Interaction for O-GlcNAc Analysis.", "journal": "ACS applied materials & interfaces", "date": "2022-10-26", "authors": "Wu Ci, Shi Song, Hou Chunyan, Luo Yang, Byers Stephen, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "title": "Cell-type-specific labeling and profiling of glycans in living mice.", "journal": "Nature chemical biology", "date": "2022-06", "authors": "Fan Xinqi, Song Qitao, Sun De-En, Hao Yi, Wang Jingyang, Wang Chunting, Chen Xing", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35513511", "url": "https://glygen.org/publication/PubMed/35513511" } ] }, { "title": "Quantitative phosphoproteomics reveals widespread full 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"reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "GlyConnect", "id": "2891", "url": "https://glyconnect.expasy.org/browser/proteins/2891" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "title": "A probability-based approach for high-throughput protein phosphorylation analysis and site localization.", "journal": "Nature biotechnology", "date": "2006", "authors": "Beausoleil SA, Villen J, Gerber SA, Rush J, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q5VT52", "url": "https://www.uniprot.org/uniprotkb/Q5VT52" }, { "database": "iPTMnet", "id": "Q5VT52-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52-1" } ], "reference": [ { "type": "PubMed", "id": "16964243", "url": "https://glygen.org/publication/PubMed/16964243" } ] }, { "title": "Quantitative phosphoproteomic analysis of T cell receptor signaling reveals system-wide modulation of protein-protein interactions.", "journal": "Science signaling", "date": "2009", "authors": "Mayya V, Lundgren DH, Hwang SI, Rezaul K, Wu L, Eng JK, Rodionov V, Han DK", "evidence": [ { "database": "UniProtKB", "id": "Q5VT52", "url": "https://www.uniprot.org/uniprotkb/Q5VT52" }, { "database": "iPTMnet", "id": "Q5VT52", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "19690332", "url": "https://glygen.org/publication/PubMed/19690332" } ] }, { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q5VT52", "url": "https://www.uniprot.org/uniprotkb/Q5VT52" }, { "database": "iPTMnet", "id": "Q5VT52-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52-1" } ], "reference": [ { "type": "PubMed", "id": "18669648", "url": "https://glygen.org/publication/PubMed/18669648" } ] }, { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "Q5VT52", "url": "https://www.uniprot.org/uniprotkb/Q5VT52" }, { "database": "iPTMnet", "id": "Q5VT52", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis.", "journal": "Science signaling", "date": "2010", "authors": "Olsen JV, Vermeulen M, Santamaria A, Kumar C, Miller ML, Jensen LJ, Gnad F, Cox J, Jensen TS, Nigg EA, Brunak S, Mann M", "evidence": [ { "database": "UniProtKB", "id": "Q5VT52", "url": "https://www.uniprot.org/uniprotkb/Q5VT52" }, { "database": "iPTMnet", "id": "Q5VT52-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52-1" } ], "reference": [ { "type": "PubMed", "id": "20068231", "url": "https://glygen.org/publication/PubMed/20068231" } ] }, { "title": "Phosphopeptide enrichment by aliphatic hydroxy acid-modified metal oxide chromatography for nano-LC-MS/MS in proteomics applications.", "journal": "Molecular & cellular proteomics : MCP", "date": "2007", "authors": "Sugiyama N, Masuda T, Shinoda K, Nakamura A, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "Q5VT52-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52-1" } ], "reference": [ { "type": "PubMed", "id": "17322306", "url": "https://glygen.org/publication/PubMed/17322306" } ] }, { "title": "Successive and selective release of phosphorylated peptides captured by hydroxy acid-modified metal oxide chromatography.", "journal": "Journal of proteome research", "date": "2008", "authors": "Kyono Y, Sugiyama N, Imami K, Tomita M, Ishihama Y", "evidence": [ { "database": "iPTMnet", "id": "Q5VT52-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52-1" } ], "reference": [ { "type": "PubMed", "id": "18767875", "url": "https://glygen.org/publication/PubMed/18767875" } ] }, { "title": "Lys-N and trypsin cover complementary parts of the phosphoproteome in a refined SCX-based approach.", "journal": "Analytical chemistry", "date": "2009", "authors": "Gauci S, Helbig AO, Slijper M, Krijgsveld J, Heck AJ, Mohammed S", "evidence": [ { "database": "iPTMnet", "id": "Q5VT52-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52-1" } ], "reference": [ { "type": "PubMed", "id": "19413330", "url": "https://glygen.org/publication/PubMed/19413330" } ] }, { "title": "Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2009", "authors": "Pan C, Olsen JV, Daub H, Mann M", "evidence": [ { "database": "iPTMnet", "id": "Q5VT52-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52-1" } ], "reference": [ { "type": "PubMed", "id": "19651622", "url": "https://glygen.org/publication/PubMed/19651622" } ] }, { "title": "Phosphorylation dynamics during early differentiation of human embryonic stem cells.", "journal": "Cell stem cell", "date": "2009", "authors": "Van Hoof D, Munoz J, Braam SR, Pinkse MW, Linding R, Heck AJ, Mummery CL, Krijgsveld J", "evidence": [ { "database": "iPTMnet", "id": "Q5VT52-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52-1" } ], "reference": [ { "type": "PubMed", "id": "19664995", "url": 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"authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic 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"title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, 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Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { 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in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification 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"https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { 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Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { 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identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": 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General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": 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"https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { 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in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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"reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, 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"https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { 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"url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, 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in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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"https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { 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"https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { 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proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { 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"https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "GlyConnect", "id": "2891", "url": "https://glyconnect.expasy.org/browser/proteins/2891" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "title": "Toward a comprehensive characterization of a human cancer cell phosphoproteome.", "journal": "Journal of proteome research", "date": "2013", "authors": "Zhou H, Di Palma S, Preisinger C, Peng M, Polat AN, Heck AJ, Mohammed S", "evidence": [ { "database": "UniProtKB", "id": "Q5VT52", "url": "https://www.uniprot.org/uniprotkb/Q5VT52" }, { "database": "iPTMnet", "id": "Q5VT52", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23186163", "url": "https://glygen.org/publication/PubMed/23186163" } ] }, { "title": "Improved titanium dioxide enrichment of phosphopeptides from HeLa cells and high confident phosphopeptide identification by cross-validation of MS/MS and MS/MS/MS spectra.", "journal": "Journal of proteome research", "date": "2007", "authors": "Yu LR, Zhu Z, Chan KC, Issaq HJ, Dimitrov DS, Veenstra TD", "evidence": [ { "database": "iPTMnet", "id": "Q5VT52-1", "url": "http://research.bioinformatics.udel.edu/iptmnet/entry/Q5VT52-1" } ], "reference": [ { "type": "PubMed", "id": "17924679", "url": "https://glygen.org/publication/PubMed/17924679" } ] }, { "title": "A quantitative atlas of mitotic phosphorylation.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2008", "authors": "Dephoure N, Zhou C, Villen J, Beausoleil SA, Bakalarski CE, Elledge SJ, Gygi SP", "evidence": [ { "database": "UniProtKB", "id": "Q5VT52", "url": "https://www.uniprot.org/uniprotkb/Q5VT52" }, 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"Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223" } ] }, { "title": "Global profiling of O-GlcNAcylated and/or phosphorylated proteins in hepatoblastoma.", "journal": "Signal transduction and targeted therapy", "date": "2019", "authors": "Song H, Ma J, Bian Z, Chen S, Zhu J, Wang J, Huang N, Yin M, Sun F, Xu M, Pan Q", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "GlyConnect", "id": "2891", "url": "https://glyconnect.expasy.org/browser/proteins/2891" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "title": "Spatial and temporal proteomics reveals the distinct distributions and dynamics of O-GlcNAcylated proteins.", "journal": "Cell reports", "date": "2022-06-14", "authors": "Xu Senhan, Tong Ming, Suttapitugsakul Suttipong, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35705054", "url": "https://glygen.org/publication/PubMed/35705054" } ] } ], "crossref": [ { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": "https://glygen.org/publication/PubMed/34725712", "database": "PubMed", "categories": [ "Other" ] }, { "id": "32119511", "url": "https://glygen.org/publication/PubMed/32119511", "database": "PubMed", "categories": [ "Other" ] }, { "id": "22661428", "url": "https://glygen.org/publication/PubMed/22661428", "database": "PubMed", "categories": [ "Other" ] }, { "id": "36240223", "url": "https://glygen.org/publication/PubMed/36240223", "database": "PubMed", "categories": 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"https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31637018", "url": "https://glygen.org/publication/PubMed/31637018" } ] }, { "title": "A Chemoenzymatic Method Based on Easily Accessible Enzymes for Profiling Protein O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": "https://glygen.org/publication/PubMed/40596516" } ] }, { "title": "Quantitative Profiling of Protein O-GlcNAcylation Sites by an Isotope-Tagged Cleavable Linker.", "journal": "ACS chemical biology", "date": "2018", "authors": "Qin K, Zhu Y, Qin W, Gao J, Shao X, Wang YL, Zhou W, Wang C, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30059200", "url": "https://glygen.org/publication/PubMed/30059200" } ] }, { "title": "Systematic Evaluation of Affinity Enrichment Methods for O-GlcNAc Proteomics.", "journal": "Journal of proteome research", "date": "2024-10-04", "authors": "Hou Chunyan, Wu Ci, Wu Zichun, Cheng Yifan, Li Weiyu, Sun Hui, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39302247", "url": "https://glygen.org/publication/PubMed/39302247" } ] }, { "title": "`Two Birds One Stone` Strategy for the Site-Specific Analysis of Core Fucosylation and O-GlcNAcylation.", "journal": "Journal of the American Chemical Society", "date": "2023-07-26", "authors": "Luo Yawen, Wang Yuqiu, Tian Yinping, Zhou Hu, Wen Liuqing", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37340703", "url": "https://glygen.org/publication/PubMed/37340703" } ] }, { "title": "A triarylphosphine-trimethylpiperidine reagent for the one-step derivatization and enrichment of protein post-translational modifications and identification by mass spectrometry.", "journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40136647", "url": "https://glygen.org/publication/PubMed/40136647" } ] }, { "title": "Quantitative proteomics identifies altered O-GlcNAcylation of structural, synaptic and memory-associated proteins in Alzheimer's disease.", "journal": "The Journal of pathology", "date": "2017", "authors": "Wang S, Yang F, Petyuk VA, Shukla AK, Monroe ME, Gritsenko MA, Rodland KD, Smith RD, Qian WJ, Gong CX, Liu T", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "28657654", "url": "https://glygen.org/publication/PubMed/28657654" } ] }, { "title": "Highly Efficient Enrichment of O-GlcNAc Glycopeptides Based on Chemical Oxidation and Reversible Hydrazide Chemistry.", "journal": "Analytical chemistry", "date": "2021", "authors": "Chen Y, Qin H, Yue X, Zhou J, Liu L, Nie Y, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional activity during breast cancer cell genotoxic adaptation.", "journal": "Biochimica et biophysica acta. General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { "title": "Mapping and Quantification of Over 2000 O-linked Glycopeptides in Activated Human T Cells with Isotope-Targeted Glycoproteomics (Isotag).", "journal": "Molecular & cellular proteomics : MCP", "date": "2018", "authors": "Woo CM, Lund PJ, Huang AC, Davis MM, Bertozzi CR, Pitteri SJ", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "Data Submission", "id": "GLY_000142", "url": "http://data.glygen.org/GLY_000142" } ], "reference": [ { "type": "PubMed", "id": "29351928", "url": "https://glygen.org/publication/PubMed/29351928" } ] }, { "title": "Endo-M Mediated Chemoenzymatic Approach Enables Reversible Glycopeptide Labeling for O-GlcNAcylation Analysis.", "journal": "Angewandte Chemie (International ed. in English)", "date": "2022", "authors": "Chen Y, Tang F, Qin H, Yue X, Nie Y, Huang W, Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35289036", "url": "https://glygen.org/publication/PubMed/35289036" } ] }, { "title": "4-Deoxy-4-fluoro-GalNAz (4FGalNAz) Is a Metabolic Chemical Reporter of O-GlcNAc Modifications, Highlighting the Notable Substrate Flexibility of O-GlcNAc Transferase.", "journal": "ACS chemical biology", "date": "2022", "authors": "Jackson EG, Cutolo G, Yang B, Yarravarapu N, Burns MWN, Bineva-Todd G, Roustan C, Thoden JB, Lin-Jones HM, van Kuppevelt TH, Holden HM, Schumann B, Kohler JJ, Woo CM, Pratt MR", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34931806", "url": "https://glygen.org/publication/PubMed/34931806" } ] }, { "title": "O-GlcNAcylation reduces proteome solubility and regulates the formation of biomolecular condensates in human cells.", "journal": "Nature communications", "date": "2025-04-30", "authors": "Xu Senhan, Yin Kejun, Xu Xing, Fu Longping, Wu Ronghu", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40307207", "url": "https://glygen.org/publication/PubMed/40307207" } ] }, { "title": "Proteome wide purification and identification of O-GlcNAc-modified proteins using click chemistry and mass spectrometry.", "journal": "Journal of proteome research", "date": "2013", "authors": "Hahne H, Sobotzki N, Nyberg T, Helm D, Borodkin VS, van Aalten DM, Agnew B, Kuster B", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "23301498", "url": "https://glygen.org/publication/PubMed/23301498" } ] }, { "title": "An Optimized Isotopic Photocleavable Tagging Strategy for Site-Specific and Quantitative Profiling of Protein O-GlcNAcylation in Colorectal Cancer Metastasis.", "journal": "ACS chemical biology", "date": "2022", "authors": "Liu J, Hao Y, Wang C, Jin Y, Yang Y, Gu J, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35254053", "url": "https://glygen.org/publication/PubMed/35254053" } ] }, { "title": "O-GlcNAc transferase regulates collagen deposition and fibrosis resolution in idiopathic pulmonary fibrosis.", "journal": "Frontiers in immunology", "date": "2024", "authors": "Vang Shia, Helton Eric Scott, Guo Yiming, Burpee Bailey, Rose Elex, Easter Molly, Bollenbecker Seth, Hirsch Meghan June, Matthews Emma Lea, Jones Luke Isaac, Howze Patrick Henry, Rajasekaran Vasanthi, Denson Rebecca, Cochran Phillip, Attah Isaac Kwame, Olson Heather, Clair Geremy, Melkani Girish, Krick Stefanie, Barnes Jarrod Wesley", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "38665916", "url": "https://glygen.org/publication/PubMed/38665916" } ] }, { "title": "Extensive crosstalk between O-GlcNAcylation and phosphorylation regulates cytokinesis.", "journal": "Science signaling", "date": "2010", "authors": "Wang Z, Udeshi ND, Slawson C, Compton PD, Sakabe K, Cheung WD, Shabanowitz J, Hunt DF, Hart GW", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" }, { "database": "GlyConnect", "id": "2891", "url": "https://glyconnect.expasy.org/browser/proteins/2891" } ], "reference": [ { "type": "PubMed", "id": "20068230", "url": "https://glygen.org/publication/PubMed/20068230" } ] }, { "title": "Simultaneously Identifying and Distinguishing Glycoproteins with O-GlcNAc and O-GalNAc (the Tn Antigen) in Human Cancer Cells.", "journal": "Analytical chemistry", "date": "2022", "authors": "Xu S, Zheng J, Xiao H, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35132862", "url": "https://glygen.org/publication/PubMed/35132862" } ] }, { "title": "Spatiotemporal Activation of Protein O-GlcNAcylation in Living Cells.", "journal": "Journal of the American Chemical Society", "date": "2022", "authors": "He J, Fan Z, Tian Y, Yang W, Zhou Y, Zhu Q, Zhang W, Qin W, Yi W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35138101", "url": "https://glygen.org/publication/PubMed/35138101" } ] }, { "title": "O-GlcNAcylation of Raptor transduces glucose signals to mTORC1.", "journal": "Molecular cell", "date": "2023-08-17", "authors": "Xu Chenchen, Pan Xiaoqing, Wang Dong, Guan Yuanyuan, Yang Wenyu, Chen Xing, Liu Ying", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "37541260", "url": "https://glygen.org/publication/PubMed/37541260" } ] }, { "title": "Cell-type-specific labeling and profiling of glycans in living mice.", "journal": "Nature chemical biology", "date": "2022-06", "authors": "Fan Xinqi, Song Qitao, Sun De-En, Hao Yi, Wang Jingyang, Wang Chunting, Chen Xing", "evidence": [ { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "35513511", "url": "https://glygen.org/publication/PubMed/35513511" } ] } ], "crossref": [ { "id": "29237092", "url": "https://glygen.org/publication/PubMed/29237092", "database": "PubMed", "categories": [ "Other" ] }, { "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52", "database": "O-GlcNAc Database", "categories": [ "Other" ] }, { "id": "30620550", "url": "https://glygen.org/publication/PubMed/30620550", "database": "PubMed", "categories": [ "Other" ] }, { "id": "39534244", "url": "https://glygen.org/publication/PubMed/39534244", "database": "PubMed", "categories": [ "Other" ] }, { "id": "34725712", "url": 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O-GlcNAcylation.", "journal": "Analytical chemistry", "date": "2020", "authors": "Xu S, Sun F, Wu R", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "32574038", "url": "https://glygen.org/publication/PubMed/32574038" } ] }, { "title": "DNA probe pulldown screening uncovers O-GlcNAcylation modulation of transcription factor DNA interactions.", "journal": "Scientific reports", "date": "2025-07-02", "authors": "Li Guofang, Meng Fanxu, Zhong Xiaomin, Yu Kairan, Zhang Nana, Zhang Keren, Huang Huang, Li Wenli, Zhang Jianing, Wang Wei, Ren Yan, Liu Yubo", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "40596516", "url": 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"journal": "Chemical communications (Cambridge, England)", "date": "2018", "authors": "Huo B, Zhang W, Zhao X, Dong H, Yu Y, Wang J, Qian X, Qin W", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "30379171", "url": "https://glygen.org/publication/PubMed/30379171" } ] }, { "title": "GATAD2B O-GlcNAcylation Regulates Breast Cancer Stem-like Potential and Drug Resistance.", "journal": "Cells", "date": "2025-03-08", "authors": "Le Minh Giang, Merzy Jessica, Esquea Emily M, Ahmed Nusaiba N, Young Riley G, Sharp Ryan J, Dhameliya Tejsi T, Agana Bernice, Lee Mi-Hye, Bethard Jennifer R, Comte-Walters Susana, Ball Lauren E, Reginato Mauricio J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": 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Ye M", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34846842", "url": "https://glygen.org/publication/PubMed/34846842" } ] }, { "title": "Proteomic profiling and genome-wide mapping of O-GlcNAc chromatin-associated proteins reveal an O-GlcNAc-regulated genotoxic stress response.", "journal": "Nature communications", "date": "2020", "authors": "Liu Y, Chen Q, Zhang N, Zhang K, Dou T, Cao Y, Liu Y, Li K, Hao X, Xie X, Li W, Ren Y, Zhang J", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "33214551", "url": "https://glygen.org/publication/PubMed/33214551" } ] }, { "title": "O-GlcNAc modification regulates MTA1 transcriptional 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General subjects", "date": "2021", "authors": "Xie X, Wu Q, Zhang K, Liu Y, Zhang N, Chen Q, Wang L, Li W, Zhang J, Liu Y", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "34019948", "url": "https://glygen.org/publication/PubMed/34019948" } ] }, { "title": "BioSITe: A Method for Direct Detection and Quantitation of Site-Specific Biotinylation.", "journal": "Journal of proteome research", "date": "2018", "authors": "Kim DI, Cutler JA, Na CH, Reckel S, Renuse S, Madugundu AK, Tahir R, Goldschmidt HL, Reddy KL, Huganir RL, Wu X, Zachara NE, Hantschel O, Pandey A", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "29249144", "url": "https://glygen.org/publication/PubMed/29249144" } ] }, { "title": "Ultradeep O-GlcNAc proteomics reveals widespread O-GlcNAcylation on tyrosine residues of proteins.", "journal": "Proceedings of the National Academy of Sciences of the United States of America", "date": "2024-11-19", "authors": "Hou Chunyan, Deng Jingtao, Wu Ci, Zhang Jing, Byers Stephen, Moremen Kelley W, Pei Huadong, Ma Junfeng", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "39531497", "url": "https://glygen.org/publication/PubMed/39531497" } ] }, { "title": "Next-generation unnatural monosaccharides reveal that ESRRB O-GlcNAcylation regulates pluripotency of mouse embryonic stem cells.", "journal": "Nature communications", "date": "2019", "authors": "Hao Y, Fan X, Shi Y, Zhang C, Sun DE, Qin K, Qin W, Zhou W, Chen X", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "31492838", "url": "https://glygen.org/publication/PubMed/31492838" } ] }, { "title": "A Novel Quantitative Mass Spectrometry Platform for Determining Protein O-GlcNAcylation Dynamics.", "journal": "Molecular & cellular proteomics : MCP", "date": "2016", "authors": "Wang X, Yuan ZF, Fan J, Karch KR, Ball LE, Denu JM, Garcia BA", "evidence": [ { "database": "O-GlcNAc Database", "id": "Q5VT52", "url": "https://www.oglcnac.mcw.edu/search/?query_protein=Q5VT52" }, { "database": "O-GlcNAc Atlas", "id": "Q5VT52", "url": "https://oglcnac.org/atlas/detail/Q5VT52" } ], "reference": [ { "type": "PubMed", "id": "27114449", "url": "https://glygen.org/publication/PubMed/27114449" } ] }, { 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"resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. 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It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma." }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of colorectum", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of large intestine", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "cancer of the large bowel", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, advanced, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colon cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer with chromosomal instability, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, somatic", "description": "" }, { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer, susceptibility to, autosomal dominant, 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"id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", 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"" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate 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Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). 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Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "CA - cancer of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "Tumour of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "malignant uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "neoplasm of uterus", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterine tumor", "description": "" }, { "id": "DOID:363", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:363", "name": "uterus neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:9460", "DOID:5166", "DOID:2021", "DOID:4114" ], "evidence": [ { "id": "363", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:363" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:1324", "recommended_name": { "id": "DOID:1324", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:1324", "name": "lung cancer", "description": "A respiratory system cancer that is located_in the lung." }, "synonyms": [ { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "A malignant neoplasm involving the lung." }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "adenocarcinoma of lung, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "cancer of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, protection against, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, resistance to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, somatic", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "lung cancer, susceptibility to, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung neoplasm", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumor", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant lung tumour", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant neoplasm of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumor of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "malignant tumour of the lung", "description": "" }, { "id": "MONDO:0008903", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0008903", "name": "nonsmall cell lung cancer, response to tyrosine kinase inhibitor in, autosomal dominant, somatic mutation", "description": "" }, { "id": "MONDO:0008903", "resource": 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"MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", 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"" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate 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It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:2531", "recommended_name": { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematologic cancer", "description": "An organ system cancer located in the hematological system that is characterized by uncontrolled cellular proliferation in blood, bone marrow and lymph nodes." }, "synonyms": [ { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic malignancy", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematologic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "Hematological tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "blood cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic and lymphoid system tumor", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic cancer", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic neoplasm", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "hematopoietic tumors", "description": "" }, { "id": "DOID:2531", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:2531", "name": "malignant hematopoietic neoplasm", "description": "" } ], "unlinked_id_list": [ "DOID:0081452", "DOID:706", "DOID:1039", "DOID:5604", "DOID:6536", "DOID:0080638", "DOID:7757", "DOID:0050743", "DOID:4960", "DOID:8527", "DOID:1036", "DOID:5772" ], "evidence": [ { "id": "2531", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:2531" } ] }, { "disease_id": "DOID:9256", "recommended_name": { "id": "DOID:9256", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:9256", "name": "colorectal cancer", "description": "A large intestine cancer that is located_in the colon and/or located_in the rectum." }, "synonyms": [ { "id": "MONDO:0005575", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0005575", "name": "colorectal cancer", "description": "A primary or metastatic malignant neoplasm that affects the colon or rectum. 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"DOID:368" ], "evidence": [ { "id": "1319", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:1319" } ] }, { "disease_id": "DOID:10283", "recommended_name": { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer", "description": "A male reproductive organ cancer that is located_in the prostate." }, "synonyms": [ { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:4159", "recommended_name": { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "skin cancer", "description": "An integumentary system cancer located_in the skin that is the uncontrolled growth of abnormal skin cells." }, "synonyms": [ { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "CA - skin cancer", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "malignant neoplasm of skin", "description": "" }, { "id": "DOID:4159", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:4159", "name": "melanoma and Non-melanoma skin cancer", "description": "" } ], "unlinked_id_list": [ "DOID:3149", "DOID:3451" ], "evidence": [ { "id": "4159", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:4159" } ] }, { "disease_id": "DOID:11054", "recommended_name": { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "urinary bladder cancer", "description": "An urinary system cancer that results_in malignant growth located_in the urinary bladder." }, "synonyms": [ { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "bladder cancer", "description": "" }, { "id": "DOID:11054", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:11054", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "urinary bladder cancer", "description": "A primary or metastatic malignant neoplasm involving the bladder." }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "tumour of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "bladder cancer, somatic", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "cancer of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder neoplasm", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumor", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant bladder tumour", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm of urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant neoplasm, urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of the urinary bladder", "description": "" }, { "id": "MONDO:0001187", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0001187", "name": "malignant tumor of urinary 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"id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "NGP - new growth of prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "hereditary prostate cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "malignant tumor of the prostate", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate cancer, familial", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostate neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic cancer", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "prostatic neoplasm", "description": "" }, { "id": "DOID:10283", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:10283", "name": "tumor of the prostate", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "HPCX1", "description": "" }, { "id": "MONDO:0010257", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010257", "name": "prostate cancer, hereditary, X-linked 1", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "HPCX2", "description": "" }, { "id": "MONDO:0010405", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0010405", "name": "prostate cancer, hereditary, X-linked 2", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the RNASEL gene." }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "RNASEL familial prostate cancer", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "familial prostate cancer caused by mutation in RNASEL", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "prostate cancer, hereditary, type 1", "description": "" }, { "id": "MONDO:0011098", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011098", "name": "HPC1", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "prostate cancer, hereditary, type 8", "description": "" }, { "id": "MONDO:0011270", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0011270", "name": "HPC8", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Distal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of Proximal Third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of abdominal esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant tumor of the middle Third of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "A primary or metastatic malignant neoplasm involving the esophagus." }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophagus cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophageal tumour", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant esophagus tumor", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": 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"MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": 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"resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", 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"name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": 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"resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] }, { "disease_id": "DOID:5041", "recommended_name": { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophageal cancer", "description": "A gastrointestinal system cancer that is located_in the esophagus." }, "synonyms": [ { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca lower third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "Ca middle third oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "esophagus cancer", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of lower third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of middle third of oesophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of proximal third of esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease Ontology", "url": "https://disease-ontology.org/term/DOID:5041", "name": "malignant neoplasm of upper third esophagus", "description": "" }, { "id": "DOID:5041", "resource": "Disease 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"https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "cancer of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal cancer, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "esophageal squamous cell carcinoma, somatic", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": 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"https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of the oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus neoplasm", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant oesophagus tumour", "description": "" }, { "id": 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}, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca lower third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "Ca middle third oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of esophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": "malignant neoplasm of distal third of oesophagus", "description": "" }, { "id": "MONDO:0007576", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0007576", "name": 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"url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, hereditary, type 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "prostate cancer, susceptibility to, 3", "description": "" }, { "id": "MONDO:0012093", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012093", "name": "HPC3", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, hereditary, type 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "prostate cancer, susceptibility to, 4", "description": "" }, { "id": "MONDO:0012094", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012094", "name": "HPC4", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "prostate cancer, hereditary, type 5", "description": "" }, { "id": "MONDO:0012244", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012244", "name": "HPC5", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "prostate cancer, hereditary, type 6", "description": "" }, { "id": "MONDO:0012300", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012300", "name": "HPC6", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "HPC7", "description": "" }, { "id": "MONDO:0012470", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012470", "name": "prostate cancer, hereditary, 7", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "prostate cancer, hereditary, type 9", "description": "" }, { "id": "MONDO:0012597", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012597", "name": "HPC9", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "HPC10", "description": "" }, { "id": "MONDO:0012620", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012620", "name": "prostate cancer, hereditary, 10", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the EHBP1 gene." }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "EHBP1 familial prostate cancer", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "familial prostate cancer caused by mutation in EHBP1", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "prostate cancer, hereditary, type 12", "description": "" }, { "id": "MONDO:0012741", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012741", "name": "HPC12", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "Any familial prostate cancer in which the cause of the disease is a mutation in the MSMB gene." }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "MSMB familial prostate cancer", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "familial prostate cancer caused by mutation in MSMB", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "prostate cancer, hereditary, type 13", "description": "" }, { "id": "MONDO:0012758", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012758", "name": "HPC13", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "HPC11", "description": "" }, { "id": "MONDO:0012768", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012768", "name": "prostate cancer, hereditary, 11", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "HPC14", "description": "" }, { "id": "MONDO:0012769", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012769", "name": "prostate cancer, hereditary, 14", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "HPC15", "description": "" }, { "id": "MONDO:0012770", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0012770", "name": "prostate cancer, hereditary, 15", "description": "" }, { "id": "MONDO:0700275", "resource": "MONDO", "url": "https://monarchinitiative.org/disease/MONDO:0700275", "name": "prostate cancer, hereditary", "description": "An instance of prostate cancer that is caused by an inherited genomic modification in an individual. Familial prostate cancer (FPC) is a malignant tumor of the prostate with an early onset. FPC is either asymptomatic or causes mictionary symptoms, erectile dysfunction, bone pain, venous compression and infectious or inflammatory syndrome (for the metastatic forms). It is also characterized by familial antecedents." }, { "id": "MIM:601518", "resource": "MIM", "url": "https://www.omim.org/entry/601518", "name": "Prostate cancer, hereditary, 1", "description": "Prostate cancer, hereditary, 1" }, { "id": "MIM:610997", "resource": "MIM", "url": "https://www.omim.org/entry/610997", "name": "Prostate cancer, hereditary, 9", "description": "Prostate cancer, hereditary, 9" }, { "id": "MIM:611868", "resource": "MIM", "url": "https://www.omim.org/entry/611868", "name": "Prostate cancer, hereditary, 12", "description": "Prostate cancer, hereditary, 12" }, { "id": "MIM:611928", "resource": "MIM", "url": "https://www.omim.org/entry/611928", "name": "Prostate cancer, hereditary, 13", "description": "Prostate cancer, hereditary, 13" }, { "id": "MIM:611955", "resource": "MIM", "url": "https://www.omim.org/entry/611955", "name": "Prostate cancer, hereditary, 11", "description": "Prostate cancer, hereditary, 11" }, { "id": "MIM:176807", "resource": "MIM", "url": "https://www.omim.org/entry/176807", "name": "Prostate cancer", "description": "Prostate cancer" } ], "unlinked_id_list": [], "evidence": [ { "id": "10283", "database": "AGR", "url": "https://www.alliancegenome.org/disease/DOID:10283" } ] } ], "keywords": [ "biomuta", "somatic", "cancer", "disease" ] } ], "all_sites": [ { "type": "glycosylation", "site_list": [ { "start_pos": "36", "end_pos": "36" }, { "start_pos": "40", "end_pos": "40" } ] }, { "type": "snv", "site_list": [ { "start_pos": "113", "end_pos": "113" }, { "start_pos": "119", "end_pos": "119" }, { "start_pos": "139", "end_pos": "139" }, { "start_pos": "167", "end_pos": "167" }, { "start_pos": "177", "end_pos": "177" }, { "start_pos": "181", "end_pos": "181" }, { "start_pos": "183", "end_pos": "183" }, { "start_pos": "192", "end_pos": "192" }, { "start_pos": "194", "end_pos": "194" }, { "start_pos": "208", "end_pos": "208" }, { "start_pos": "292", "end_pos": "292" }, { "start_pos": "307", "end_pos": "307" }, { "start_pos": 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